The Missa Papae Marcelli consists, like most Renaissance masses, of a Kyrie, Gloria, Credo, Sanctus/Benedictus, and Agnus Dei, though the Agnus Dei is in two parts rather than the common three. The mass is freely composed, not based upon a cantus firmus or parody. Perhaps because of this, the mass is not as thematically consistent as Palestrina's masses based on models. It is a six-voice mass, though the use of the full forces is reserved for specific climactic portions in the text, and voice combinations are varied throughout the piece. It is set primarily in a homorhythmic, declamatory style, with little overlapping of text and a general preference for block chords such that the text, unlike many polyphonic masses of the 16th century, can clearly be heard in performance. Like much of Palestrina's contrapuntal work, voices move in primarily stepwise motion, and the voice leading strictly follows the rules of the diatonic modes codified by theorist Gioseffo Zarlino.
The third and closing sessions of the Council of Trent were held in 1562-63, at which the use of polyphonic music in the Catholic Church was discussed. Concerns were raised over two problems: first, the use of music that was objectionable, such as secular songs provided with religious lyrics (contrafacta) or masses based on songs with lyrics about drinking or lovemaking; and second, whether imitation in polyphonic music obscured the words of the mass, interfering with the listener's devotion. Some debate occurred over whether polyphony should be banned outright in worship, and some of the auxiliary publications by attendants of the Council caution against both of these problems. However, none of the official proclamations from the Council mentions polyphonic music, excepting one injunction against the use of music that is, in the words of the Council, "lascivious or impure".
Starting in the late 16th century, a legend began that the second of these points, the threat that polyphony might have been banned by the Council because of the unintelligibility of the words, was the impetus behind Palestrina's composition of this mass. It was believed that the simple, declamatory style of Missa Papae Marcelli convinced Cardinal Carlo Borromeo, on hearing, that polyphony could be intelligible, and that music such as Palestrina's was all too beautiful to ban from the Church. In 1607, the composer Agostino Agazzari wrote:
Jesuit musicians of the 17th century maintained this rumor, and it made its way into music history books into the 19th century, when historian Giuseppe Baini, in his 1828 biography of Palestrina, couched him as the "savior of polyphony" from a council wishing to wipe it out entirely:
An entry in the papal chapel diaries confirms that a meeting such as the one described by Baini occurred, but no mention is made of whether the Missa Papae Marcelli was performed there or what the reaction of the audience was. This legend persisted into the 20th century; Hans Pfitzner's opera Palestrina is based upon this understanding of the deliberations of the Tridentine officials. While Palestrina sympathized with many of the Council's decisions, and, like Vincenzo Ruffo, sought deliberately to compose in a simplified, easily-understood style to please church officials, there is no evidence to support either the view that the Council sought to banish polyphony entirely or that Palestrina's mass was the deciding factor in changing their minds.
In the latter part of the 20th century, the Missa Papae Marcelli has been recorded frequently, and is often used as a model for the study of stile antico Renaissance polyphony in university courses on music.